THE USE OF SIMULATIONS IN EVOLUTIONARY POPULATION GENETICS: APPLICATIONS ON HUMANS, OWLS AND VIRTUAL ORGANISMS

Summary (in English) Computer simulations provide a practical way to address scientific questions that would be otherwise intractable. In evolutionary biology, and in population genetics in particular, the investigation of evolutionary processes frequently involves the implementation of complex models, making simulations a particularly valuable tool in the area. In this thesis work, I explored three questions involving the geographical range expansion of populations, taking advantage of spatially explicit simulations coupled with approximate Bayesian computation. First, the neutral evolutionary history of the human spread around the world was investigated, leading to a surprisingly simple model: A straightforward diffusion process of migrations from east Africa throughout a world map with homogeneous landmasses replicated to very large extent the complex patterns observed in real human populations, suggesting a more continuous (as opposed to structured) view of the distribution of modern human genetic diversity, which may play a better role as a base model for further studies. Second, the postglacial evolution of the European barn owl, with the formation of a remarkable coat-color cline, was inspected with two rounds of simulations: (i) determine the demographic background history and (ii) test the probability of a phenotypic cline, like the one observed in the natural populations, to appear without natural selection. We verified that the modern barn owl population originated from a single Iberian refugium and that they formed their color cline, not due to neutral evolution, but with the necessary participation of selection. The third and last part of this thesis refers to a simulation-only study inspired by the barn owl case above. In this chapter, we showed that selection is, indeed, effective during range expansions and that it leaves a distinguished signature, which can then be used to detect and measure natural selection in range-expanding populations. Résumé (en français) Les simulations fournissent un moyen pratique pour répondre à des questions scientifiques qui seraient inabordable autrement. En génétique des populations, l'étude des processus évolutifs implique souvent la mise en oeuvre de modèles complexes, et les simulations sont un outil particulièrement précieux dans ce domaine. Dans cette thèse, j'ai exploré trois questions en utilisant des simulations spatialement explicites dans un cadre de calculs Bayésiens approximés (approximate Bayesian computation : ABC). Tout d'abord, l'histoire de la colonisation humaine mondiale et de l'évolution de parties neutres du génome a été étudiée grâce à un modèle étonnement simple. Un processus de diffusion des migrants de l'Afrique orientale à travers un monde avec des masses terrestres homogènes a reproduit, dans une très large mesure, les signatures génétiques complexes observées dans les populations humaines réelles. Un tel modèle continu (opposé à un modèle structuré en populations) pourrait être très utile comme modèle de base dans l'étude de génétique humaine à l'avenir. Deuxièmement, l'évolution postglaciaire d'un gradient de couleur chez l'Effraie des clocher (Tyto alba) Européenne, a été examiné avec deux séries de simulations pour : (i) déterminer l'histoire démographique de base et (ii) tester la probabilité qu'un gradient phénotypique, tel qu'observé dans les populations naturelles puisse apparaître sans sélection naturelle. Nous avons montré que la population actuelle des chouettes est sortie d'un unique refuge ibérique et que le gradient de couleur ne peux pas s'être formé de manière neutre (sans l'action de la sélection naturelle). La troisième partie de cette thèse se réfère à une étude par simulations inspirée par l'étude de l'Effraie. Dans ce dernier chapitre, nous avons montré que la sélection est, en effet, aussi efficace dans les cas d'expansion d'aire de distribution et qu'elle laisse une signature unique, qui peut être utilisée pour la détecter et estimer sa force.

Molecular genetics of "PRPF31" dominant mutations linked to retinitis pigmentosa

ABSTRACT : The retina is one of the most important human sensory tissues since it detects and transmits all visual information from the outside world to the brain. Retinitis pigmentosa (RP) is the name given to a group of inherited diseases that affect specifically the photoreceptors present in the retina and in many instances lead to blindness. Dominant mutations in PRPF31, a gene that encodes for a pre-mRNA splicing factor, cause retinitis pigmentosa with reduced penetrance. We functionally investigated a novel mutation, identified in a large family with autosomal dominant RP, and 7 other mutations, substitutions and microdeletions, in 12 patients from 7 families with PRPF31-linked RP. Seven mutations lead to PRPF31 mRNA with premature stop codons and one to mRNA lacking the exon containing the initiation codon. Quantification of PRPF31 mRNA and protein levels revealed a significant reduction in cell lines derived from patients, compared to non carriers of mutations in PRPF31. Allelic quantification of PRPF31 mRNA indicated that the level of mutated mRNA is very low compared to wild-type mRNA. No mutant protein was detected and the subnuclear localization of wild-type PRPF31 remains the same in cell lines from patients and controls. Blocking nonsense-mediated mRNA decay in cell lines derived from patients partially restored PRPF31 mutated mRNA but derived proteins were still undetectable, even when protein degradation pathways were inhibited. Our results demonstrated that the vast majority of PRPF31 mutations result in null alleles, since they are subject to surveillance mechanisms that degrade mutated mRNA and possibly block its translation. Altogether, these data indicate that the likely cause of PRPF31-linked RP is haploinsufficiency, rather than a dominant negative effect. Penetrance of PRPF31 mutations has been previously demonstrated to be inversely correlated with the level of PRPF31 mRNA, since high expression of wild-type PRPF31 mRNA protects from the disease. Consequently, we have investigated the genetic modifiers that control the expression of PRPF31 by quantifying PRPF31 mRNA levels in cell lines derived from 200 individuals from 15 families representative of the general population. By linkage analyses we identified a 8.2Mb-region on chromosome 14q21-23 that contains a gene involved in the modulation of PRPF31 expression. We also assessed apreviously-mapped penetrance factor invariably located on the wild-type allele and linked to the PRPF31 locus in asymptomatic patients from different families with RP. We demonstrated that this modifier increases the expression of both PRPF31 alleles already at the pre-mRNA level. Finally, our data suggest that PRPF31 mRNA expression and consequently the penetrance of PRPF31 mutations is modulated by at least 2 diffusible compounds, which act on both PRPF31 alleles during their transcription.

Opportunity to shape the prevention and management of obesity

Cooperation and Working Together (CAWT), the cross border health and social care partnership has been working with the Departments of Health to progress a three year cross border obesity prevention and management project aimed at families. They have been successful in securing funding from the EU INTERREG IVA programme. A planning workshop focussing on this will be held on Friday 26 June 2009.

Obesity Weighting up the Evidence: All-Island Multisectoral Conference on Obesity

The World Health Organization reports that overweight and obesity have reached epidemic proportions globally and estimates that approximately 1.6 billion adults and at least 20 million children under the age of five are overweight or obese. It is accepted that being overweight or obese increases the risk of health conditions such as heart disease, stroke, diabetes and some cancers and has significant impacts on a wide range of other factors including education, employment and emotional wellbeing. This conference aimed to present a multisectoral audience with the latest developments in overweight and obesity prevention and management. This presentation was given by Dr. Kevin Balanda, Institute of Public Health in Ireland. The Institute of Public Health in Ireland (IPH) is leading the development of an All-Ireland obesity observatory The obesity observatory development is being undertaken in collaboration with: - HRB Centre for Health and Diet Research ﾖ UCC /UCD - Centre of Excellence for Public Health (NI) - QUB Projected outcomes: Adequate sample size Data to be sought and recorded Usefulness of a database in influencing policy Value to clinicians in management of obesity

IPH response to DHSSPS obesity prevention framework consultation 'A Fitter Future for All'

Preventing obesity is a key priority for the Department of Health, Social Services and Public Safety (DHSSPS) in Northern Ireland. In support of this, the DHSSPS has led the development of a cross-Departmental, crosssectoral Obesity Prevention Framework for Northern Ireland 2011-2021, entitled A Fitter Future For All, which seeks to reduce the prevalence of overweight and obesity throughout  Northern Ireland. The Framework focuses action on three main pillars: food & nutrition; physical activity; and data and research, and within the context of three life course stages: Early Years; Children and Young People; and Adults. This approach is consistent with the responses being undertaken by a number of countries, following the Foresight Report.

Obesity markers and estimated 10-year fatal cardiovascular risk in Switzerland.

BACKGROUND AND AIM: There is an ongoing debate on which obesity marker better predicts cardiovascular disease (CVD). In this study, the relationships between obesity markers and high (>5%) 10-year risk of fatal CVD were assessed. METHODS AND RESULTS: A cross-sectional study was conducted including 3047 women and 2689 men aged 35-75years. Body fat percentage was assessed by tetrapolar bioimpedance. CVD risk was assessed using the SCORE risk function and gender- and age-specific cut points for body fat were derived. The diagnostic accuracy of each obesity marker was evaluated through receiver operating characteristics (ROC) analysis. In men, body fat presented a higher correlation (r=0.31) with 10-year CVD risk than waist/hip ratio (WHR, r=0.22), waist (r=0.22) or BMI (r=0.19); the corresponding values in women were 0.18, 0.15, 0.11 and 0.05, respectively (all p<0.05). In both genders, body fat showed the highest area under the ROC curve (AUC): in men, the AUC (95% confidence interval) were 76.0 (73.8-78.2), 67.3 (64.6-69.9), 65.8 (63.1-68.5) and 60.6 (57.9-63.5) for body fat, WHR, waist and BMI, respectively. In women, the corresponding values were 72.3 (69.2-75.3), 66.6 (63.1-70.2), 64.1 (60.6-67.6) and 58.8 (55.2-62.4). The use of the body fat percentage criterion enabled the capture of three times more subjects with high CVD risk than the BMI criterion, and almost twice as much as the WHR criterion. CONCLUSION: Obesity defined by body fat percentage is more related with 10-year risk of fatal CVD than obesity markers based on WHR, waist or BMI.

IPH gives evidence to NI Assembly Health Committee Inquiry into Obesity

IPH Chief Executive, Dr Jane Wilde gave evidence to the Northern Ireland Assembly Health Committee inquiry into obesity. Dr Wilde recommended the following: Supporting the Department of Health’s strategic approach based on an understanding of the nature and complexity of obesity. Urgent and short term action to coordinate current activities and ensure focus on the most vulnerable. Exploring new forms and incentives to promote cross departmental work. Setting intermediate outcomes and targets Building stronger links between research, policy and practice, for example asking the Health Committee to set up a round table of researchers and policy makers Working systematically and transparently to identify key areas for cooperation with UK, Ireland and Europe Drawing from IPH work and other research, Dr Wilde briefed the Health Committee on the extent and impact of obesity, reasons for rising levels of obesity and the need for a stronger strategic response. She highlighted the importance of cross government action, the responsibilities of those beyond the health sector and the need for stronger evidence-informed policy and practice.

Narcolepsy and familial advanced sleep-phase syndrome: molecular genetics of sleep disorders.

Sleep disorders are very prevalent and represent an emerging worldwide epidemic. However, research into the molecular genetics of sleep disorders remains surprisingly one of the least active fields. Nevertheless, rapid progress is being made in several prototypical disorders, leading recently to the identification of the molecular pathways underlying narcolepsy and familial advanced sleep-phase syndrome. Since the first reports of spontaneous and induced loss-of-function mutations leading to hypocretin deficiency in human and animal models of narcolepsy, the role of this novel neurotransmission pathway in sleep and several other behaviors has gained extensive interest. Also, very recent studies using an animal model of familial advanced sleep-phase syndrome shed new light on the regulation of circadian rhythms.

Framework for Preventing and Addressing Overweight and Obesity in Northern Ireland 2012-2022: A Fitter Future for All (PDF 1MB)

A Framework for Preventing and Addressing Overweight and Obesity in NI 2012-2022 This Framework aims to “empower the population of Northern Ireland to make healthy choices, reduce the risk of overweight and obesity related diseases and improve health and wellbeing, by creating an environment that supports and promotes a physically active lifestyle and a healthy diet”. In addition, the following overarching targets have been set: Adults • To reduce the level of obesity by 4% and overweight and obesity by 3% by 2022. Children • A 3% reduction of obesity and 2% reduction of overweight and obesity by 2022åÊThe target is in two parts; the proportion that are obese and the proportion that are overweight and obese. Prevention is typically taken forward through action to address two main areas – improving diet and nutrition, and increasing participation in physical activity. Acknowledging this, two overarching objectives for the Framework have been set: to increase the percentage of people eating a healthy, nutritionally balanced diet; and to increase the percentage of the population meeting the CMO guidelines on physical activity.

Rôle de l'inactivité physique dans l'étiologie de l'obésité [The role of physical inactivity in the etiology of obesity].

The activity-related energy expenditure mainly depends upon body weight, the type, intensity and duration of the exercise as well as the mechanical efficiency with which the subjects perform the work. Controversy still exist about the role of hypoactivity in the aetiology of obesity both in adolescence and adulthood. A number of experimental studies based on indirect assessment of physical activity (such as pedometers, accelerometers, cinematography and heart rate) have demonstrated a significant reduction in spontaneous physical activity in certain obese groups as compared to lean matched controls. On the other hand, direct measurements of energy expenditure (by indirect calorimetry) have shown a linear relationship between body weight and 24-hour (or activity-related) energy expenditure. It therefore appears that despite the greater placidity characterising some grossly obese subjects, the absolute rate of energy expenditure - particularly in weight bearing activities - is not lower than in lean subjects, since the hypoactivity does not fully compensate for the greater gross energy cost of a given activity.

A 600 kb deletion syndrome at 16p11.2 leads to energy imbalance and neuropsychiatric disorders.

BACKGROUND: The recurrent ~600 kb 16p11.2 BP4-BP5 deletion is among the most frequent known genetic aetiologies of autism spectrum disorder (ASD) and related neurodevelopmental disorders. OBJECTIVE: To define the medical, neuropsychological, and behavioural phenotypes in carriers of this deletion. METHODS: We collected clinical data on 285 deletion carriers and performed detailed evaluations on 72 carriers and 68 intrafamilial non-carrier controls. RESULTS: When compared to intrafamilial controls, full scale intelligence quotient (FSIQ) is two standard deviations lower in carriers, and there is no difference between carriers referred for neurodevelopmental disorders and carriers identified through cascade family testing. Verbal IQ (mean 74) is lower than non-verbal IQ (mean 83) and a majority of carriers require speech therapy. Over 80% of individuals exhibit psychiatric disorders including ASD, which is present in 15% of the paediatric carriers. Increase in head circumference (HC) during infancy is similar to the HC and brain growth patterns observed in idiopathic ASD. Obesity, a major comorbidity present in 50% of the carriers by the age of 7 years, does not correlate with FSIQ or any behavioural trait. Seizures are present in 24% of carriers and occur independently of other symptoms. Malformations are infrequently found, confirming only a few of the previously reported associations. CONCLUSIONS: The 16p11.2 deletion impacts in a quantitative and independent manner FSIQ, behaviour and body mass index, possibly through direct influences on neural circuitry. Although non-specific, these features are clinically significant and reproducible. Lastly, this study demonstrates the necessity of studying large patient cohorts ascertained through multiple methods to characterise the clinical consequences of rare variants involved in common diseases.

Directory of Familial Cancer Genetics Specialist Teams

The Directory of Familial Cancer Genetics Specialist Teams has been produced under the auspices of the Northern Ireland Regional Advisory Committee on Cancer. It contains details of the full membership of the clinical teams providing care in each of Health and Social Services Board Area. Lead Clinicians for Familial Cancer Genetics Service (PDF 58 KB) Eastern (PDF 68 KB) Northern (PDF 61 KB) Southern (PDF 62 KB) Western (PDF 11 KB) The Directory will be updated on an annual basis. Please e-mail amendments to:- irene.wilkinson@dhsspsni.gov.uk

Thermogenic effects of commercially available plant preparations aimed at treating human obesity.

Different commercially available plant preparations have been claimed to have anti-obesity action. We investigated the acute effects of oral administration of 12 of these preparations in non-obese women and men. No significant increase in energy expenditure (EE) has been noted after treatment with any of these preparations. No change in respiratory quotient (RQ) was shown, except after treatment with maté (Ilex paraguariensis) extract, where a drop in RQ was observed, indicating a rise in the proportion of fat oxidized. The results suggested the poor potential of these plant preparations in the treatment of obesity, except possibly for the maté extract. Further studies are required to explore the influence of higher dosages of these preparations as well as chronic administration in man.

Blunted glucose-induced thermogenesis in 'overweight' patients: a factor contributing to relapse of obesity.

Glucose-induced thermogenesis was studied in 12 overweight patients (9F and 3M) before (mean body weight +/- s.e.m. 83 +/- 2 kg) and after weight loss (68 +/- 2 kg), and in eight of the same patients following relapse of body weight gain (84 +/- 5 kg). Expressed as a percentage of the energy content of the 100 g oral glucose load, glucose-induced thermogenesis was lower in the overweight before weight loss (6.5 +/- 0.5 per cent, P less than 0.05), after weight loss (3.9 +/- 0.6 per cent, P less than 0.01) and after weight regain (6.3 +/- 0.9 per cent, P less than 0.05) than in a group of lean control subjects, matched for sex and age (8.3 +/- 0.5 per cent). Basal energy expenditure was lower after weight reduction than before (1.16 +/- 0.04 vs 1.41 +/- 0.08 kcal/min, P less than 0.01). In the formerly overweight patients, the combined effect of a decreased basal energy expenditure and an attenuation of glucose induced thermogenesis resulted in a postprandial energy expenditure which was markedly lower than in the overweight state (P less than 0.001). Following relapse of obesity, glucose-induced thermogenesis remained attenuated compared to control subjects. These results suggest that a lowered basal energy expenditure and a reduced glucose-induced thermogenesis contribute to the positive energy balance which results in relapse of body weight gain after cessation of a hypocaloric diet.